Variant report

Variant	rs2420880
Chromosome Location	chr2:73087265-73087266
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:72997728..72998659-chr2:73086602..73087607,8	MCF-7	breast:
2	chr2:73086659..73087605-chr2:73114661..73115372,2	K562	blood:
3	chr2:72998078..72998669-chr2:73086603..73087704,4	MCF-7	breast:
4	chr2:72997752..72999020-chr2:73086588..73087576,7	K562	blood:
5	chr2:73051752..73054246-chr2:73085621..73088585,2	MCF-7	breast:
6	chr2:73086760..73087512-chr3:168166411..168167083,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144036	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10211019	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1027848	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496186	0.92[CEU][hapmap]
rs10865393	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11126385	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1150500	1.00[CEU][hapmap]
rs1161265	1.00[CEU][hapmap]
rs1161267	1.00[CEU][hapmap]
rs11684985	0.85[CEU][hapmap]
rs11894160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12474728	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622275	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12713775	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12989141	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12996406	0.92[CEU][hapmap]
rs13035731	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1567230	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995734	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2048170	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	0.92[CEU][hapmap]
rs2135985	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420881	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420883	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2421095	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4321391	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852298	0.91[CEU][hapmap]
rs4852893	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4852902	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546782	0.92[CEU][hapmap]
rs6546783	0.92[CEU][hapmap]
rs6546786	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546788	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546789	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546790	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546791	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546792	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6730083	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6739002	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6750740	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6758431	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6758542	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7571064	0.84[CEU][hapmap]
rs7580268	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7586787	0.94[EUR][1000 genomes]
rs7588602	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7592155	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs925146	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925147	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925148	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990569	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2420880	CYP26B1	cis	Whole Blood	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73079000-73088200	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:73082200-73088200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73082600-73088000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr2:73085000-73088200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:73085000-73089200	Weak transcription	Fetal Heart	heart
6	chr2:73087000-73089200	Weak transcription	Brain Angular Gyrus	brain
7	chr2:73087000-73089200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:73087200-73087400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:73087200-73087600	Bivalent Enhancer	A549	lung
10	chr2:73087200-73088200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:73087200-73089200	Weak transcription	NHEK	skin

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